| layout | title | parent | grand_parent | nav_order | toc | summary | permalink |
|---|---|---|---|---|---|---|---|
default |
MSREACT Example 1 |
MSREACT Examples |
Examples and Guides |
1 |
false |
An example for generating EI-MS fragments for an organic molcecule. |
/page/examples/msreact/example_1.html |
{: .no_toc }
{{ page.summary }} {: .fs-6 .fw-300 }
. {: .test-justify }
{% include image.html file="msreact-example-1-1.png" alt="Bacillaene at GFN-FF level" caption="Most stable gas-phase structure of 2-pentanone at charge +1 with GFN2-xTB." max-width=400 %}
We want to investigate the fragmentation reactions of 2-pentanone in an EI-MS experiment. Therefore, we provide the lowest conformer found by CREST at charge +1 as input <2-pentanone.xyz>. We only want to get unique fragments so we use the -msmolbar flag to sort out duplicates with molbar. Before starting crest, we should make sure that molbar is properly installed and can be executed globally.
{: .text-justify }
{{ site.data.icons.code }}
command
{{ site.data.icons.codefile }} 2-pentanone.xyz
{{ site.data.icons.codefile }} crest_msreact_products.xyz
{{ site.data.icons.checkfile }} output
{% include command.html cmd='crest 2-pentanone.xyz --msreact --chrg 1 --msmolbar --T 16
' %}
{% capture struc_file %}
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{% capture struc_file %}
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H 4.5756131115 -0.6389345542 -0.3540199922
16
-19.28633 p20
C -2.3064510223 -0.2935703106 0.2316341300
C -0.8406840997 0.2342446552 0.2241972607
H 3.3049133769 0.4621729747 0.5006836879
H -0.6308954107 0.4638168639 1.2962608946
H 1.9417212879 0.0963091851 1.6824489167
H -2.9602227985 0.4909619585 0.6125923226
H -2.6209211216 -0.5219620455 -0.7875178709
H -2.3829272315 -1.1796495961 0.8552161901
C 0.1462068662 -0.9549831778 -0.1436948056
H 1.4793123349 0.3962475243 -1.1843023630
O -0.6507943876 1.2719943437 -0.5147218652
C 1.5428743178 -0.4170729821 -0.4299728364
H 0.1482331952 -1.6788065370 0.6700978027
H -0.2474755987 -1.4352489065 -1.0428788581
C 2.3100479668 0.0782355835 0.6676339017
H 2.1460974775 -1.1604202715 -0.9836869472
16
-19.28607 p21
C -2.3536922058 -0.2937212350 0.0055427168
C -0.8924914984 0.0952310083 0.0130111990
H 3.1580794035 0.5664929575 -0.2244177735
H 1.5276113053 1.3521065029 -0.3576005103
H 2.0887781682 0.7482028814 1.2675377098
H -2.9678468253 0.6018418975 -0.0550292000
H -2.5698131418 -0.9472453101 -0.8374478615
H -2.5820950132 -0.8288955909 0.9268041574
C 0.0344041832 -0.9861384719 -0.0966430374
H 1.7315247357 -1.0520933437 -1.3032283980
O -0.5488310196 1.2660805062 0.1088137563
C 1.4939699531 -0.8256334409 -0.2438531435
H 2.1015873909 0.9540079812 2.2375608517
H -0.3616887560 -1.9873741122 -0.1706003283
C 2.1022244456 0.5100946092 0.0265792086
H 2.0049231585 -1.6278278422 0.3087611486
16
-19.27595 p22
C -2.3259913419 -0.2565058186 -0.0271690390
C -0.9129636333 0.1826484579 0.0846463998
H 3.0594427560 0.6868818695 -0.3699544844
H 1.4146702761 1.3300133336 0.0362790291
H 2.2845624708 0.4501224675 1.2199291376
H -2.9822004653 0.5299048064 0.3443822087
H -2.5553174107 -0.4089789750 -1.0838998743
H -2.5160562524 -1.1892923298 0.4990234055
C 0.1000872464 -1.0302742357 0.1086335042
H 3.1113089849 -2.1443971887 -2.0529132782
O -0.5325734180 1.3092589419 0.1531679506
C 1.4321759205 -0.6818818243 -0.3526429235
H 0.1103751342 -1.2618247941 1.1828153764
H -0.3309533291 -1.8767251038 -0.4254612640
C 2.1225141220 0.4752793932 0.1348644412
H 1.9029109657 -1.2791858843 -1.1658128859
16
-19.26206 p23
C -2.3872580991 -0.2870273935 0.0378224780
C -0.9137980270 -0.0581931091 -0.0044238458
H 3.4905550411 1.7982746191 -0.1492899351
H 1.7782207571 2.4959206504 0.0881590690
H 2.6758783953 1.7079407015 1.5172684341
H -2.9136966494 0.6645087214 0.0909069897
H -2.6827289690 -0.7903010909 -0.8851591812
H -2.6683338167 -0.9224745597 0.8747762534
C -0.0507562563 -1.3028197488 0.3189033074
H 0.9779436156 -1.1745857227 -1.6246791032
O -0.3877758507 0.9879976602 -0.2522085028
C 1.0416244868 -1.5167370553 -0.6041557483
H 0.3076155374 -1.2096862287 1.3518228211
H -0.6949020752 -2.1976720846 0.3081100245
C 2.6413384834 1.9877194502 0.4807996635
H 1.9387254452 -2.0288116539 -0.2966640615
16
-19.25628 p24
C -2.2766561980 -0.2456755170 -0.0049608234
C -0.9362811415 0.1622426375 0.0696925032
H 3.0816773564 0.6835861925 -0.2437515693
H 1.5142665570 1.3576414276 0.2348293655
H 2.3392077672 0.2065324665 1.2978634038
H -3.0268175582 0.4770948425 -0.2477404332
H -1.2859189862 -2.2502590765 -0.9632135969
H -2.5970912044 -1.2501649207 0.2040511855
C 0.1106087947 -0.9603415689 0.1640055013
H 1.2950517199 -0.3847510067 -1.5283328612
O -0.5449555121 1.3228320213 0.0602888617
C 1.4281346187 -0.6742017465 -0.4812836906
H 0.1818573012 -1.3497639149 1.1821936865
H -0.4789431300 -1.8893926065 -0.4808064800
C 2.1414706828 0.4568214661 0.2560446150
H 2.0588617667 -1.5702480865 -0.4537632383
16
-19.22329 p25
C -2.5930152127 -0.6050724513 -0.0688172605
C -1.1812590628 -0.3582034131 -0.0416719060
H 1.1271529491 2.1544391897 -0.8670022688
H 0.7549507255 2.4392355112 0.6782110267
H 1.8111505835 0.6146002558 1.4292661169
H -3.1475257986 0.2120918081 0.3988671845
H -2.9184711489 -0.6225529584 -1.1163684992
H -2.8849992238 -1.5573202352 0.3910829559
C -0.0524360060 -1.2279498559 0.1329501357
H 1.2375777327 -0.4297391346 -1.4168058851
O 0.7651767786 1.7661011798 -0.0387982373
C 1.3073302537 -0.6085483129 -0.3424657857
H 0.0422815570 -1.4688357269 1.2013711694
H -0.1953375731 -2.1819214762 -0.3947901782
C 1.6745733239 0.6302354217 0.3603600517
H 2.0941070069 -1.3414871861 -0.1688508340
{% endcapture %}
{% include codecell.html content=struc_file style="text-align:justify" %}
{% capture output_file %}
{% include defaulttab.html id="open-1" %}
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║ ___ ___ ___ ___ _____ ║
║ / __| _ \ __/ __|_ _| ║
║ | (__| / _|\__ \ | | ║
║ \___|_|_\___|___/ |_| ║
║ ║
║ Conformer-Rotamer Ensemble Sampling Tool ║
║ based on the xTB methods ║
║ ║
╚════════════════════════════════════════════╝
Version 3.0pre, Di 27. Feb 18:07:37 CET 2024
commit (9967345) compiled by 'gorges@joey'
Cite work conducted with this code as
• P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192. • S.Grimme, JCTC, 2019, 15, 2847-2862.
for works involving QCG cite
• S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme, JCTC, 2022, 18 (5), 3174-3189. • C.Plett, S. Grimme, Angew. Chem. Int. Ed. 2023, 62, e202214477.
for works involving MECP screening cite
• P.Pracht, C.Bannwarth, JCTC, 2022, 18 (10), 6370-6385.
Original code P.Pracht, S.Grimme, Universität Bonn, MCTC with help from (alphabetical order): C.Bannwarth, F.Bohle, S.Ehlert, G.Feldmann, J.Gorges, S.Grimme, C.Plett, P.Pracht, S.Spicher, P.Steinbach, P.Wesolowski, F.Zeller
Online documentation is available at https://crest-lab.github.io/crest-docs/
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License (LGPL) for more details.
Command line input:
crest 2-pentanone.xyz --msreact --chrg 1 -T 16 --msmolbar
--chrg 1 -T 16 (CPUs/Threads selected)
Setting up backup calculator ... done.
User-defined calculation level: : xTB calculation via tblite lib : GFN2-xTB level : Molecular charge : 1 : Fermi temperature : 300.00000 : Accuracy : 1.00000 : max SCC cycles : 500 : Weight : 1.00000
======================================== | | | MSREACT | | automated MS fragment generator | | | | University of Bonn, MCTC |
S. Grimme, P. Pracht, J. Gorges.
Cite work conducted with this code as
Philipp Pracht, Stefan Grimme, Christoph Bannwarth, Fabian Bohle, Sebastian Ehlert, Gereon Feldmann, Johannes Gorges, Marcel Müller, Tim Neudecker, Christoph Plett, Sebastian Spicher, Pit Steinbach, Patryk A. Wesolowski, and Felix Zeller J. Chem. Phys., 2024, submitted.
Input energy successfully calculated. msinput is:,
LMO calculation ... done. Protonation sides at atom positions: 11 2 Add attractive potential for H-shifts:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 done. Detect fragments Remaining structures: 78 Calling molbar for sorting out duplicates by molbar sorted out 53 fragments accoding to topology check number of products is now: 25 Calling CREGEN routine and sort out structures above energy window of 200.0000 kcal/mol CREGEN> running RMSDs ... done. reading product structures file crest_msreact_products.xyz Remaining structures after cregen: 25 Detect fragments writing isomers to "isomers.xyz" and fragmentpairs to "fragmentpairs.xyz" writing products to "crest_msreact_products.xyz"
number of printed structures: 25 directory | fragment type | rel. energy [kcal/mol] fragmentpair: | sumformula | molecular mass p1 isomer -9.34756891 p2 isomer -2.14258043 p3 isomer 1.86697294 p4 isomer 3.89151930 p5 isomer 12.73758939 p6 isomer 16.10644930 p7 isomer 17.84348965 p8 isomer 19.42084767 p9 isomer 28.13638323 p10 fragmentpair 32.51972516 p10f1 H9C5O1 85.12455 p10f2 H1 1.00794 p11 fragmentpair 33.82916173 p11f1 H6C3O1 58.07926 p11f2 H4C2 28.05323 p12 fragmentpair 36.49854311 p12f1 H3C2O1 43.04470 p12f2 H7C3 43.08779 p13 isomer 47.37567939 p14 isomer 48.32906081 p15 isomer 48.67965662 p16 isomer 48.69211896 p17 fragmentpair 50.10495027 p17f1 H3C1 15.03456 p17f2 H7C4O1 71.09793 p18 isomer 54.81903989 p19 fragmentpair 54.83785263 p19f1 H5C3O1 57.07132 p19f2 H5C2 29.06118 p20 isomer 59.30044273 p21 fragmentpair 59.46567225 p21f1 H9C5O1 85.12455 p21f2 H1 1.00794 p22 fragmentpair 65.81406637 p22f1 H9C5O1 85.12455 p22f2 H1 1.00794 p23 fragmentpair 74.53288381 p23f1 H7C4O1 71.09793 p23f2 H3C1 15.03456 p24 fragmentpair 78.15987602 p24f1 H9C5O1 85.12455 p24f2 H1 1.00794 p25 isomer 98.86011463
Number of generated isomers: 16 Number of generated fragmentpairs: 9
- wall-time: 0 d, 0 h, 0 min, 16.607 sec
- cpu-time: 0 d, 0 h, 0 min, 11.144 sec
- ratio c/w: 0.671 speedup
- Total number of energy+grad calls: 1
CREST terminated normally.
{% endcapture %} {% include codecell.html content=output_file style="text-align:justify" %}
CREST produces 25 unique products and writes them sorted according to their relative energy to the file crest_msreact_products.xyz. Additionally, isomers are written to isomers.xyz, fragmentpairs to fragmentpairs.xyz.
{: .text-justify }